p5-transdecoder: Upgrade to 5.3.0
This commit is contained in:
Jason Bacon
parent
e46ac3379a
commit
a096bce2a9
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@ -8,11 +8,11 @@
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# p5-URI-ESC?
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# FIXME: Check use statements in all perl scripts for more deps
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DISTNAME= p5-transdecoder-${PORTVERSION}
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DISTNAME= p5-transdecoder-${PV}
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CATEGORIES= biology
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MASTER_SITES= ${MASTER_SITE_GITHUB:=TransDecoder/}
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GITHUB_PROJECT= TransDecoder
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GITHUB_TAG= ${PORTVERSION}
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GITHUB_TAG= TransDecoder-v${PV}
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MAINTAINER= bacon@NetBSD.org
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HOMEPAGE= http://transdecoder.github.io/
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@ -27,23 +27,23 @@ SUBST_SED.path+= -e 's|$$FindBin::RealBin/util|${PREFIX}/libexec/TransDecoder/ut
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SUBST_FILES.path+= ${WRKSRC}/TransDecoder*
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SUBST_FILES.path+= ${WRKSRC}/util/*.pl
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DEPENDS= cdhit>=4.6.1:../../biology/cdhit \
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DEPENDS= cdhit>=4.6.8:../../wip/cdhit \
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p5-URI>=0:../../www/p5-URI
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USE_TOOLS= perl
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REPLACE_BASH= sample_data/runMe.sh util/pfam_mpi.pbs
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REPLACE_PERL= util/*.pl sample_data/*.pl PerlLib/*.pm \
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REPLACE_PERL= util/*.pl sample_data/*.pl PerlLib/*.pm PerlLib/*.ph \
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TransDecoder.LongOrfs TransDecoder.Predict
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NO_BUILD= yes
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PORTVERSION= 2.0.1
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PV= 5.3.0
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INSTALLATION_DIRS= bin lib/TransDecoder/PerlLib libexec/TransDecoder/util
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do-install:
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${INSTALL_SCRIPT} ${WRKSRC}/PerlLib/* \
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${DESTDIR}${PREFIX}/lib/TransDecoder/PerlLib
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${INSTALL_SCRIPT} ${WRKSRC}/TransDecoder* ${DESTDIR}${PREFIX}/bin
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${INSTALL_SCRIPT} ${WRKSRC}/TransDecoder.LongOrfs ${WRKSRC}/TransDecoder.Predict ${DESTDIR}${PREFIX}/bin
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${INSTALL_SCRIPT} ${WRKSRC}/util/*.pl \
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${DESTDIR}${PREFIX}/libexec/TransDecoder/util
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@ -1,26 +1,43 @@
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@comment $NetBSD$
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bin/TransDecoder.LongOrfs
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bin/TransDecoder.Predict
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lib/TransDecoder/PerlLib/DelimParser.pm
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lib/TransDecoder/PerlLib/Fasta_reader.pm
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lib/TransDecoder/PerlLib/GFF3_utils.pm
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lib/TransDecoder/PerlLib/Fasta_retriever.pm
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lib/TransDecoder/PerlLib/GFF3_utils2.pm
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lib/TransDecoder/PerlLib/GTF.pm
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lib/TransDecoder/PerlLib/GTF_utils2.pm
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lib/TransDecoder/PerlLib/Gene_obj.pm
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lib/TransDecoder/PerlLib/Gene_obj_indexer.pm
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lib/TransDecoder/PerlLib/Longest_orf.pm
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lib/TransDecoder/PerlLib/Nuc_translator.pm
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lib/TransDecoder/PerlLib/TiedHash.pm
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lib/TransDecoder/PerlLib/Overlap_piler.pm
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lib/TransDecoder/PerlLib/PWM.pm
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lib/TransDecoder/PerlLib/Pipeliner.pm
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lib/TransDecoder/PerlLib/Process_cmd.pm
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lib/TransDecoder/PerlLib/overlapping_nucs.ph
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libexec/TransDecoder/util/cdna_alignment_orf_to_genome_orf.pl
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libexec/TransDecoder/util/compute_base_probs.pl
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libexec/TransDecoder/util/cufflinks_gtf_genome_to_cdna_fasta.pl
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libexec/TransDecoder/util/cufflinks_gtf_to_alignment_gff3.pl
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libexec/TransDecoder/util/cufflinks_gtf_to_bed.pl
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libexec/TransDecoder/util/exclude_similar_proteins.pl
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libexec/TransDecoder/util/fasta_prot_checker.pl
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libexec/TransDecoder/util/ffindex_resume.pl
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libexec/TransDecoder/util/gene_list_to_gff.pl
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libexec/TransDecoder/util/get_FL_accs.pl
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libexec/TransDecoder/util/get_longest_ORF_per_transcript.pl
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libexec/TransDecoder/util/get_top_longest_fasta_entries.pl
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libexec/TransDecoder/util/gff3_file_to_bed.pl
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libexec/TransDecoder/util/gff3_file_to_proteins.pl
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libexec/TransDecoder/util/index_gff3_files_by_isoform.pl
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libexec/TransDecoder/util/gff3_gene_to_gtf_format.pl
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libexec/TransDecoder/util/gtf_genome_to_cdna_fasta.pl
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libexec/TransDecoder/util/gtf_to_alignment_gff3.pl
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libexec/TransDecoder/util/gtf_to_bed.pl
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libexec/TransDecoder/util/nr_ORFs_gff3.pl
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libexec/TransDecoder/util/pfam_runner.pl
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libexec/TransDecoder/util/refine_gff3_group_iso_strip_utrs.pl
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libexec/TransDecoder/util/refine_hexamer_scores.pl
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libexec/TransDecoder/util/remove_eclipsed_ORFs.pl
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libexec/TransDecoder/util/score_CDS_liklihood_all_6_frames.pl
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libexec/TransDecoder/util/seq_n_baseprobs_to_logliklihood_vals.pl
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libexec/TransDecoder/util/score_CDS_likelihood_all_6_frames.pl
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libexec/TransDecoder/util/select_best_ORFs_per_transcript.pl
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libexec/TransDecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl
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libexec/TransDecoder/util/start_codon_refinement.pl
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libexec/TransDecoder/util/train_start_PWM.pl
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libexec/TransDecoder/util/uri_unescape.pl
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@ -1,6 +1,6 @@
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$NetBSD$
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SHA1 (p5-transdecoder-2.0.1.tar.gz) = 1a36aa7ecb3af9e984eb9bee818871093fa1ab74
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RMD160 (p5-transdecoder-2.0.1.tar.gz) = d59644fc9f44f428ae5f001543e33ca3b7539aec
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SHA512 (p5-transdecoder-2.0.1.tar.gz) = fd12aeda089a12036e288e58eb0a3c3b9bb1f104f6821102d84ba6ddaec1a9dd32ec7937cd87129ff9814c7c8e26b6b98d27c6af8edd7ed6b5335c4878f649de
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Size (p5-transdecoder-2.0.1.tar.gz) = 9925281 bytes
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SHA1 (p5-transdecoder-5.3.0.tar.gz) = a615b4004aa81ebcc59472feeefafde09755b093
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RMD160 (p5-transdecoder-5.3.0.tar.gz) = bbf692ecba4a2eb2b45733badfc22dc636cd07c4
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SHA512 (p5-transdecoder-5.3.0.tar.gz) = c8f6458ca09831d91a583c0abdb09398493fa1dbc4d63c5f859db12a8005b1b7861c3b6836f59a4947a9b17b660adcc496e7c3805457a21a2572ecbd05de0449
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Size (p5-transdecoder-5.3.0.tar.gz) = 15699957 bytes
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